LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -39.483817 0.0000000) to (27.917095 39.483817 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7663332 5.2961960 4.3599177 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -39.483817 0.0000000) to (27.917095 39.483817 4.3599177) create_atoms CPU = 0.001 seconds 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7663332 5.2961960 4.3599177 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -39.483817 0.0000000) to (27.917095 39.483817 4.3599177) create_atoms CPU = 0.001 seconds 330 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 5 atoms, new total = 655 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_152208847456_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.267 | 5.267 | 5.267 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4015.2199 0 -4015.2199 88517.023 116 0 -4242.8943 0 -4242.8943 2709.0566 Loop time of 36.4179 on 1 procs for 116 steps with 655 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4015.21992486382 -4242.89005272606 -4242.894286248 Force two-norm initial, final = 406.73474 0.32282096 Force max component initial, final = 109.29288 0.11923386 Final line search alpha, max atom move = 0.93543226 0.11153520 Iterations, force evaluations = 116 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.344 | 36.344 | 36.344 | 0.0 | 99.80 Neigh | 0.060788 | 0.060788 | 0.060788 | 0.0 | 0.17 Comm | 0.0069276 | 0.0069276 | 0.0069276 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006406 | | | 0.02 Nlocal: 655.000 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3871.00 ave 3871 max 3871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48648.0 ave 48648 max 48648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48648 Ave neighs/atom = 74.271756 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.267 | 5.267 | 5.267 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -4242.8943 0 -4242.8943 2709.0566 9611.6431 120 0 -4242.9534 0 -4242.9534 6616.7008 9593.6253 Loop time of 1.16448 on 1 procs for 4 steps with 655 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4242.894286248 -4242.95293818085 -4242.9534310827 Force two-norm initial, final = 47.794826 0.47485008 Force max component initial, final = 46.992974 0.12756537 Final line search alpha, max atom move = 0.00017845707 2.2764942e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1634 | 1.1634 | 1.1634 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019836 | 0.00019836 | 0.00019836 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008831 | | | 0.08 Nlocal: 655.000 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3879.00 ave 3879 max 3879 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48790.0 ave 48790 max 48790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48790 Ave neighs/atom = 74.488550 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.405 | 5.405 | 5.405 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4242.9534 0 -4242.9534 6616.7008 Loop time of 1.635e-06 on 1 procs for 0 steps with 655 atoms 244.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.635e-06 | | |100.00 Nlocal: 655.000 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3879.00 ave 3879 max 3879 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49054.0 ave 49054 max 49054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49054 Ave neighs/atom = 74.891603 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.405 | 5.405 | 5.405 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -4242.9534 -4242.9534 27.843066 78.967634 4.363315 6616.7008 6616.7008 5.3058205 19846.716 -1.9191756 2.4478997 1347.4988 Loop time of 1.791e-06 on 1 procs for 0 steps with 655 atoms 167.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.791e-06 | | |100.00 Nlocal: 655.000 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3879.00 ave 3879 max 3879 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24527.0 ave 24527 max 24527 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49054.0 ave 49054 max 49054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49054 Ave neighs/atom = 74.891603 Neighbor list builds = 0 Dangerous builds = 0 655 -4242.9534310827 eV 2.4478996587075 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:38